8RLK

Structure of the apo form of PIB-1 in an Orthorombic space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: other
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Ligand Structure Quality Assessment 


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Literature

A new type of Class C beta-lactamases defined by PIB-1. A metal-dependent carbapenem-hydrolyzing beta-lactamase, from Pseudomonas aeruginosa: Structural and functional analysis.

Medrano, F.J.Hernando-Amado, S.Martinez, J.L.Romero, A.

(2024) Int J Biol Macromol : 134298-134298

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.134298
  • Primary Citation of Related Structures:  
    8RLJ, 8RLK, 8RLL

  • PubMed Abstract: 

    Antibiotic resistance is one of most important health concerns nowadays, and β-lactamases are the most important resistance determinants. These enzymes, based on their structural and functional characteristics, are grouped in four categories (A, B, C and D). We have solved the structure of PIB-1, a Pseudomonas aeruginosa chromosomally-encoded β-lactamase, in its apo form and in complex with meropenem and zinc. These crystal structures show that it belongs to the Class C β-lactamase group, although it shows notable differences, especially in the Ω- and P2-loops, which are important for the enzymatic activity. Functional analysis showed that PIB-1 is able to degrade carbapenems but not cephalosporins, the typical substrate of Class C β-lactamases, and that its catalytic activity increases in the presence of metal ions, especially zinc. They do not bind to the active-site but they induce the formation of trimers that show an increased capacity for the degradation of the antibiotics, suggesting that this oligomer is more active than the other oligomeric species. While PIB-1 is structurally a Class C β-lactamase, the low sequence conservation, substrate profile and its metal-dependence, prompts us to position this enzyme as the founder of a new group inside the Class C β-lactamases. Consequently, its diversity might be wider than expected.


  • Organizational Affiliation

    Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain. Electronic address: fjmedrano@cib.csic.es.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Class C beta-lactamase-related serine hydrolase
A, B, C, D, E
A, B, C, D, E, F
391Pseudomonas aeruginosaMutation(s): 0 
Gene Names: CAZ10_27720DT376_01770GUL26_24405
UniProt
Find proteins for A0A1J0J3U4 (Pseudomonas aeruginosa)
Explore A0A1J0J3U4 
Go to UniProtKB:  A0A1J0J3U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1J0J3U4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MER (Subject of Investigation/LOI)
Query on MER

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
Q [auth D]
(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid
C17 H27 N3 O5 S
DYQHXZPAIVAJRU-HTXLXMOSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
M [auth B]
N [auth B]
R [auth D]
I [auth A],
J [auth A],
M [auth B],
N [auth B],
R [auth D],
S [auth E],
T [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.89α = 90
b = 101.452β = 90
c = 267.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2020-113521RB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release